I have successfully used SuperDuper in the past, but something has gone bonkers since I got my new Western Digital My Book Studio Edition (Mac).

Old setup: 1 usb external hard drive used for SuperDuper to clone to. Restores are successful and are bootable from restarts.

New setup: Still using the hard drive from old setup, but now is used for general storage. New hard drive uses firewire 800 and has two partitions: one for time capsule and the other (you've guessed it) for SuperDuper.